The inheritance of type 2 diabetes mellitus (T2DM) and obesity is likely oligogenic, i.e. determined by multiple genes. Therefore, individual susceptibility genes with small effects may remain obscured in family-based linkage studies, but could be detected in a genome-wide association scan. We have previously reported the application of the amplified fragment length polymorphism (AFLP) technique in a genome-wide search for markers that may be associated with diabetes or obesity in the Pima Indians. Subsequently, we designed a modification of the AFLP procedure to isolate new polymorphic markers from the 1q21-q23 genomic region linked with type 2 diabetes in Pimas (see project ZO1-DK69073). This approach was based on a capture of AFLP fragments using large genomic clones (bacterial artificial chromosomes, BACs) spanning 1q21-q23, and analyzing such markers for differences differences between diabetic and non-diabetic Pimas. However, with the recent completion of the human genome draft sequence and availability of numerous SNPs covering all chromosomes, the AFLP capture approach was not a cost- and time-effective strategy in comparison to using publicly available markers. Therefore, we have decided to terminate this project.